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- PDB-3au0: Structural and biochemical characterization of ClfB:ligand intera... -

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Basic information

Entry
Database: PDB / ID: 3au0
TitleStructural and biochemical characterization of ClfB:ligand interactions
ComponentsClumping factor B
KeywordsCELL ADHESION / IgG-like / Adhesin / Cytokeratin / Fibrinogen
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide ...Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.45 Å
AuthorsGanesh, V.K. / Barbu, E.M. / Deivanayagam, C.C.S. / Le, B. / Anderson, A.S. / Matsuka, Y. / Lin, S.L. / Foster, T.F. / Narayana, S.V.L. / Hook, M.
CitationJournal: To be published
Title: Structural and biochemical characterization of ClfB:ligand interactions
Authors: Ganesh, V.K. / Barbu, E.M. / Deivanayagam, C.C.S. / Le, B. / Anderson, A.S. / Matsuka, Y. / Lin, S.L. / Foster, T.F. / Narayana, S.V.L. / Hook, M.
History
DepositionJan 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clumping factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4593
Polymers37,4101
Non-polymers492
Water3,243180
1
A: Clumping factor B
hetero molecules

A: Clumping factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9176
Polymers74,8202
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3360 Å2
ΔGint-0 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.360, 96.360, 84.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Clumping factor B / Fibrinogen receptor B / Fibrinogen-binding protein B


Mass: 37409.953 Da / Num. of mol.: 1 / Fragment: N2 and N3 domain (UNP RESIDUES 203-541) / Mutation: D444E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: clfB, SA2423 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A382
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.7M sodium formate, 1.44M sodium citrate, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→63.38 Å / Num. all: 15061 / Num. obs: 14750 / Observed criterion σ(F): 2 / Biso Wilson estimate: 35.5 Å2
Reflection shellResolution: 2.45→2.6 Å / % possible all: 9.2

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.45→63.38 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1729747.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1498 10.2 %RANDOM
Rwork0.203 ---
obs0.203 14750 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3277 Å2 / ksol: 0.360879 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.45→63.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 2 180 2821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it12.341.5
X-RAY DIFFRACTIONc_mcangle_it10.352
X-RAY DIFFRACTIONc_scbond_it16.292
X-RAY DIFFRACTIONc_scangle_it14.922.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 219 9.2 %
Rwork0.234 2162 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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